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• DNA-methylation variability in normal mucosa of patients with adenomatous polyps: a marker of field cancerization

  A study linking DNA methylation modifications in the normal mucosa of the right colon in individuals with adenomatous polyp formation

  Study EGAS00001007666

• bulk Exome-seq of the 5 HCC patients which also have the single cell T cell RNA-seq data

  bulk Exome-seq data of the 5 HCC patinets. Single cell RNA seq data of these patients was under the accession number EGAD00001003337

  Dataset EGAD00001004149

• Somatic point mutation data from microsatellite unstable colorectal cancers

  The dataset contains the somatic point mutation data from the exome-targeted region of 36 exome or whole genome sequenced microsatellite unstable colorectal cancers and the somatic point mutation data from 93 additional MiSeq sequenced microsatellite unstable colorectal cancers.

  Dataset EGAD00001004281

• johannesburg_20150706_X

  Genotype data and (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 750 individuals from Respiratory and Meningeal Pathogens Unit in Soweto, South Africa - X chromosome.

  Dataset EGAD00010002580

• NanoString raw data

  NanoString raw data for a noeadjuvant combination PD-L1 plus CTLA-4 blockade trial on patients with cisplatin-ineligible operable urothelial carcinoma. All samples were FFPE tumor samples. Raw probe count data (.RCC files) were generated from nCounter Digital Analyzer (4.0.0.3).

  Dataset EGAD00010001852

• Sequencing data for oesophageal and related samples - BOs release 3 (RNA)

  Dataset EGAD00001003901

• Whole genome bisufite sequencing for smoking and non-smoking mother-child pairs

  WGBS data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years.

  Dataset EGAD00001000366

• Sci Trans Med - Mouliere et al, 2018. Non-ovarian cancer samples - STM4

  fastq files for shallow whole genome sequencing data as described in Mouliere et al, 2018. Files are those not included in STM2 i.e. these are largely non-ovarian cancer samples

  Dataset EGAD00001006132

• Genome-wide data Iberian Roma

  VCF file with genome-wide data for 62 Iberian Roma samples.

  Dataset EGAD00001006358

• Cell-free DNA TAPS provides multimodal information for early cancer detection

  TAPS data from 21 patients with HCC, 23 patients with PDAC, 30 non-cancer controls, 4 patients with cirrhosis, and 7 patients with pancreatitis.

  Dataset EGAD00001006871

• TPM matrix

  TPM matrices of counts from RNAseq data for IMvigor010 from bulk pre-treatment tumors.

  Dataset EGAD00001007653

• Target pilot trial

  In vitro and in vivo drug screens of tumor cells identify novel therapies for high-risk child cancer

  Dataset EGAD00001008358

• Raw data for "Spatial and temporal transcriptomics of medulloblastoma with chromothripsis identifies multiple genetic clones that resist to treatment and lead to relapse"

  FASTQ files from Illumina sequencing of 10x Visium experiments.

  Dataset EGAD00001010260

• Dataset for WES PCNSL

  WES sequencing of 23 samples from PCNSL tumor and blood control samples. Sequencing was performed on a NovaSeq 6000 and NextSeq 500 using Agilent SureSelectXT HS Human All Exon V7 and V8. Sequencing was always paired.

  Dataset EGAD00001010847

• WGS data for medulloblastoma samples (SJMB)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003126

• Low-coverage whole genome sequencing data to study "A biobank of patient-derived pediatric brain tumor models"

  Low-coverage whole genome sequencing data for 30 PDOX models (28 early passages, 4 late passages (2 overlaps)), 3 cell lines, and 21 matching human tumors

  Dataset EGAD00001003545

• Genomic Profiling of Sequentially Acquired Metastatic Sites from an "Exceptional Responder" Lung Adenocarcinoma Patient Reveals Extensive Genomic Heterogeneity and Novel Somatic Variants

  We employed next-generation sequencing to identify somatic alterations in multiple metastatic sites from an "exceptional responder" lung adenocarcinoma patient during his seven year course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ~1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies demonstrated increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy due to L869R mutation and increased migration due to ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a sub-clone metastasized early from the primary site and evolved independently in lymph nodes.

  Study phs001159

• Chromatin accessibility in stem cells unveils progressive transcriptional reprogramming in myelodysplastic syndrome

  Myelodysplastic syndromes (MDS) originate from hematopoietic stem cell (HSC) clones with acquired gene mutations/deletions. However, our knowledge on the epigenetic properties of MDS stem cells are limited. Here, we examined chromatin accessibility of MDS stem cells. Chromatin accessibility profiles of MDS stem cells represented the disease status better than progenitor cells and unveiled the process of stem cell reprograming during disease progression. Characterization of differentially accessible regions (DARs) revealed that MDS stem cells acquire progenitor-like chromatin accessibility with disease progression, resulting in imprecise stem-progenitor hierarchy. Profiling of transcriptional factor binding motifs at DARs revealed precocious inactivation and activation of HSC and myeloid transcriptional networks, respectively, in MDS stem cells. Increased chromatin accessibility at CEBP target sites well represented the myeloid reprograming of MDS stem cells and stratified MDS into distinct subgroups. Newly developed "Progenitor scores" based on chromatin accessibility well stratified the disease status and correlated with prognosis. These results highlight that the chromatin properties of MDS stem cells define the cell-autonomous behavior of MDS and disease progression.

  Study JGAS000718

• Human lymphoid-neutrophil/monocyte restriction co-ordinately activates increased proliferation despite parallel heterogeneity in transcriptional changes

  Recent studies indicate the human lympho-myeloid restriction process to be a different and more heterogeneous one than historically inferred. Here we describe the development of bulk and clonal culture systems that efficiently support early B-lymphoid differentiation and their use to identify biological and molecular changes that accompany their initial restriction from subsets of CD34+ human cord blood cells with lympho-myeloid-limited potential. Analyses of the changes observed revealed the acquisition of B-lymphoid- and neutrophil/monocyte (NM)-restricted properties are accompanied by a concomitantly accelerated and lineage-shared cell cycling activity and loss of self-renewal properties. Parallel, single-cell transcriptome analysis identified reduced expression of multiple self-renewal-associated genes and an accompanying heterogeneous activation of lineage-regulatory modules during the production of B, NM and dendritic cell precursors. These results uncover a connected regulation of lineage-shared proliferation control with persistent heterogeneity in the biological and transcriptional changes in the same cells undergoing B and NM lineage restriction.

  Study EGAS50000000278

• A Dormant TIL Phenotype Defines Non-Small Cell Lung Carcinomas Sensitive to Immune Checkpoint Blockers

  The biological determinants of sensitivity and resistance to immune checkpoint inhibitors are not completely understood. To elucidate the role of intratumoral T-cells and its association with the tumor genomic landscape, we perform paired whole exome DNA sequencing and multiplexed quantitative immunofluorescence (QIF) in pre-treatment samples from non-small cell lung carcinoma patients treated with PD-1 axis blockers. QIF was used to simultaneously measure the level of CD3+ tumor infiltrating lymphocytes (TILs), in situ T-cell proliferation (Ki-67 in CD3) and effector capacity (Granzyme-B in CD3). Whole exome sequencing reported in the number/type of mutations and predicted class I and class II mutant neoantigens.

  Study phs001618

• Neurodevelopment_Nantes_hospital

  The neurodevelopmental team in the genetics unit of Nantes hospital focus on the identification on new genes causing neurodevelopmental disorders through whole-genome and transcriptomics sequencing.

  Dac EGAC50000000542

• GWAS membranous nephropathy Stanescu et al., 2011 UK cohort, chr2 region of interest, imputed

  334 biopsy-confirmed membranous nephropathy (MN) cases and 349 ethnically matched healthy controls: the British cohort of the Stanescu et al., 2011 GWAS. Genotyped and imputed region of interest on chromosome 2 (hg19 chr2:160500000-161500000), as used to determine Neanderthal introgression near the PLA2R1 MN risk locus (lead SNP: rs4664308).

  Study EGAS00001007700

• RNA sequencing of genetically modified human iPSCs modeling patients with autism spectrum disorders (ASD)

  We generated two genetically modified iPSC lines. In each line, a single promoter variant identified in a patient with autism spectrum disorder (ASD) was introduced by using the CRISPR/Cas9 system. These mutant lines were analyzed by RNA-seq together with control lines to assess the impact of the introduced variant.

  Study JGAS000651

• R compatible Seurat's objetc .rds files with count data and metadata from single cell RNA seq analysis to characterize the prostate cancer tumoral microenviroment of 31 fusion biopses.

  Pre-processed Seurat objects with cellular and functional annotation information from the scRNAseq study on PC fusion biopsy samples. The data consists of rds files composed of normalised counts matrices, normalised and scaled counts, functional enrichment counts at the cellular level and metadata with patient grouping and cellular annotation variables. There are 3 .rds files, one with the total cells (SCP_data_analysis), with the selection of cells annotated as cancerous (selected_cancer_analysis) and cancer-associated fibroblasts (selected_caf_analysis).

  Dataset EGAD50000001298

• Cancer Genome Project Exome Sequencing

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Dataset EGAD00001000289